652 research outputs found
[V4Mo3O14(NAr)(3)(mu(2)-NAr)(3)](2-): the first polyarylimido-stabilized molybdovanadate cluster
No full textThe first molybdovanadate cluster with a polyarylimido trimetal fragment, [V4Mo3O14(NAr)(3)(mu(2)-NAr)(3)](2-), was in situ synthesized by using (TBA)(3)[H3V10O28] as proton and vanadium sources. Additional aniline hydrochlorides will give rise to the formation of phenyl guanidines, which will serve as cations and proton donors to form chain-like and dimeric supermolecules via H-bonding.National Natural Science Foundation of China (NSFC) [21225103, 21471087, 21221062]; State Key Laboratory of Natural and Biomimetic Drugs; Specialized Research Fund for the Doctoral Program of Higher Education of China; Beijing Natural Science Foundation [2144051]; Tsinghua University Initiative Foundation Research Program [20131089204]SCI(E)ARTICLE172551-25545
Half-Sandwich Imido into related complexes of niobium and tantulum - relative of the zirconocene family
No full textThis thesis describes studies directed towards the preparation of half- sandwich niobium and tantalirai compounds containing imido and phosphino-carbene ligands, with particular emphasis on the relationship of such species with bent metallocene complexes of the Group 4 triad. Chapter 1 highlights areas of transition metal chemistry of relevance to the general theme of this thesis, including reviews of metal imido and zirconocene chemistry. Chapter 2 describes the use of silylated anilines for convenient solution syntheses of half-sandwich imido complexes of niobium and tantalum of the type Cp'M(N-2,6-(^i)Pr(_2)-C(_6)H(_3))Cl(_2)(Cp' = Cp, Cp*). In addition, the syntheses and reactivities of mono- and bis-alkyl derivatives (methyl, neopentyl, and benzyl) are presented. The bis-neopentyl complexes CpNb(NR)(CH(_2)CMe(_3))(_2) (R = CMe(_3); 2,6-(^i)Pr(_2)-C(_6)H(_3)), reveal multiple a-agostic interactions which have been primarily studied via an X-ray crystal structure determination and NMR spectroscopy. Thermolysis of Cp*Nb(N-2,6-(^i)Pr(_2)-C(_6)H(_3))(CH(_2)Ph)(_2) in die presence of PMe(_3) affords die benzylidene complex Cp*Nb(N-2,6-(^i)Pr(_2)-C(_6)H(_3))(η(^1)-CHPh)(PMe3) whose X-ray crystal structure has been determined. Chapter 3 describes the preparation of the niobium and tantalum imido complexes Cp'M(N-2,6-(^i)Pr(_2)-C(_6)H(_3))(L)(PMe(_3)) (M = Nb, L = C(_2)H(_4), C(_3)H(_6), CO, Me(_2)C(_2). Ph(_2)C(_2), C(_6)H(_4), PMe(_3); M = Ta, L = C(_2)H(_4), C(_3)H(_6), CO). Single crystal structure determinations on CpNb(N-2,6-(^i)Pr(_2)-C(_6)H(_3))(η(^2)-C(_3)H(_6))(PMe(_3)) and CpNb(N-2,6-(^i)Pr(_2)-C(_6)H(_3))(η(_2)-C(_6)H(_4))(PMe(_3)) have been undertaken and their relationship to Group 4 metallocenes noted. Treatment of Cp*Ta(N-2,6-(^i)Pr(_2)-C(_6)H(_3))(L)(PMe(_3)) (L = C(_2)H(_4),C(_3)H(_6)) with a-olefins was found to lead to displacement of PMe(_3) and the generation of tantallacycle containing species. Chapter 4 compares the reactivity of tantalum imido and phosphino-carbenederivatives of the form Cp*Ta(E)(H)(X)(PMe(_3)) (E = N-2,6-(^i)Pr2-C(_6)H(_3), η(^2)-CHPMe(_2); X = H, I) with a number of a-olefins. Investigations into die mechanism of catalytic oligomerisation of a-olefins by Cp*Ta(η(^2)-CHPMe(_2))(H)(_2)(PMe(_3)) reveal that pathways involving metallacycle intermediates are most probable, whereas Cp*Ta(N-2,6-(^i);Pr(_2)-C(_6)H(_3))(H)(_2)(PMe(_3)) reacts with a-olefins to afford stable tantallacycle complexes. The reactivity of die dihydrido species has been moderated by the preparation of mono- iodide derivatives and their reactivity towards a-olefins studied. Cp*Ta(η(^2)-CHPMe(_2))(H)(I)(PMe(_3)) dimerises ediylene selectively to but-1-ene, while Cp*Ta(N-2,6-(^i)Pr(_2)-C(_6)H(_3))(H)(I)(PMe(_3)) reacts with ethylene to form die stable ethyl species Cp*Ta(N-2,6-(^i)Pr(_2)-C(_6)H(_3))(Et)(I). Furtherrmore, studies investigating a variety of niobium and tantalum imido species as possible catalysts for die oligomerisation and polymerisation of a-olefins under industrially relevant conditions have been undertaken in collaboration with B.P. Chemicals Ltd.. Chapter 5 gives experimental details for chapter 2-4
The protein that binds to DNA base J in trypanosomatids has features of a thymidine hydroxylase
No full text© 2007 The Author et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/
by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in Nucleic Acids Research 35 (2007): 2107-2115, doi:10.1093/nar/gkm049.Trypanosomatids contain an unusual DNA base J (ß-D-glucosylhydroxymethyluracil), which replaces a fraction of thymine in telomeric and other DNA repeats. To determine the function of base J, we have searched for enzymes that catalyze J biosynthesis. We present evidence that a protein that binds to J in DNA, the J-binding protein 1 (JBP1), may also catalyze the first step in J biosynthesis, the conversion of thymine in DNA into hydroxymethyluracil. We show that JBP1 belongs to the family of Fe2+ and 2-oxoglutarate-dependent dioxygenases and that replacement of conserved residues putatively involved in Fe2+ and 2-oxoglutarate-binding inactivates the ability of JBP1 to contribute to J synthesis without affecting its ability to bind to J-DNA. We propose that JBP1 is a thymidine hydroxylase responsible for the local amplification of J inserted by JBP2, another putative thymidine hydroxylase.This work was funded by a grant from the Netherlands Organization for Scientific Research and Chemical Sciences (NWO-CW) to P.B., NIH grant A1063523 to R.S. and NIH grant GM063584 to R.P.H
Synthesis and structural characterization of cyclic aryl ethers.
No full textThe facile preparation of macrocyclic ethers is achieved using S NAr reactions of (dichlorobenzene)CpFe + complexes with various dinucleophiles, followed by photolytic demetallation; X-ray crystallography gives unequivocal structural proof for one of these macrocycles
DNASU plasmid and PSI:Biology-Materials repositories: resources to accelerate biological research
No full textabstract: The mission of the DNASU Plasmid Repository is to accelerate research by providing high-quality, annotated plasmid samples and online plasmid resources to the research community through the curated DNASU database, website and repository (http://dnasu.asu.edu or http://dnasu.org). The collection includes plasmids from grant-funded, high-throughput cloning projects performed in our laboratory, plasmids from external researchers, and large collections from consortia such as the ORFeome Collaboration and the NIGMS-funded Protein Structure Initiative: Biology (PSI:Biology). Through DNASU, researchers can search for and access detailed information about each plasmid such as the full length gene insert sequence, vector information, associated publications, and links to external resources that provide additional protein annotations and experimental protocols. Plasmids can be requested directly through the DNASU website. DNASU and the PSI:Biology-Materials Repositories were previously described in the 2010 NAR Database Issue (Cormier, C.Y., Mohr, S.E., Zuo, D., Hu, Y., Rolfs, A., Kramer, J., Taycher, E., Kelley, F., Fiacco, M., Turnbull, G. et al. (2010) Protein Structure Initiative Material Repository: an open shared public resource of structural genomics plasmids for the biological community. Nucleic Acids Res., 38, D743–D749.). In this update we will describe the plasmid collection and highlight the new features in the website redesign, including new browse/search options, plasmid annotations and a dynamic vector mapping feature that was developed in collaboration with LabGenius. Overall, these plasmid resources continue to enable research with the goal of elucidating the role of proteins in both normal biological processes and disease.The final version of this article, as published in Nucleic Acids Research, can be viewed online at: https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkt106
An efficient system for selectively altering genetic information within mRNAs
No full text© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nucleic Acids Research 44 (2016): e157, doi:10.1093/nar/gkw738.Site-directed RNA editing (SDRE) is a strategy to precisely alter genetic information within mRNAs. By linking the catalytic domain of the RNA editing enzyme ADAR to an antisense guide RNA, specific adenosines can be converted to inosines, biological mimics for guanosine. Previously, we showed that a genetically encoded iteration of SDRE could target adenosines expressed in human cells, but not efficiently. Here we developed a reporter assay to quantify editing, and used it to improve our strategy. By enhancing the linkage between ADAR's catalytic domain and the guide RNA, and by introducing a mutation in the catalytic domain, the efficiency of converting a UAG premature termination codon (PTC) to tryptophan (UGG) was improved from ∼11% to ∼70%. Other PTCs were edited, but less efficiently. Numerous off-target edits were identified in the targeted mRNA, but not in randomly selected endogenous messages. Off-target edits could be eliminated by reducing the amount of guide RNA with a reduction in on-target editing. The catalytic rate of SDRE was compared with those for human ADARs on various substrates and found to be within an order of magnitude of most. These data underscore the promise of site-directed RNA editing as a therapeutic or experimental tool.National Institutes of Health [1R0111223855,
1R01NS64259]; Cystic Fibrosis Foundation Therapeutics
[Rosent14XXO]; Infrastructural support was
provided by the National Institutes of Health [NIGMS
1P20GM103642, NIMHD 8G12-MD007600]; National
Science Foundation [DBI 0115825, DBI 1337284]; Department
of Defense [52680-RT-ISP]
SumoPred-PLM: human SUMOylation and SUMO2/3 sites Prediction using Pre-trained Protein Language Model
No full textSUMOylation is an essential post-translational modification system with the ability to regulate nearly all aspects of cellular physiology. Three major paralogues SUMO1, SUMO2 and SUMO3 form a covalent bond between the small ubiquitin-like modifier with lysine residues at consensus sites in protein substrates. Biochemical studies continue to identify unique biological functions for protein targets conjugated to SUMO1 versus the highly homologous SUMO2 and SUMO3 paralogues. Yet, the field has failed to harness contemporary AI approaches including pre-trained protein language models to fully expand and/or recognize the SUMOylated proteome. Herein, we present a novel, deep learning-based approach called SumoPred-PLM for human SUMOylation prediction with sensitivity, specificity, Matthew's correlation coefficient, and accuracy of 74.64%, 73.36%, 0.48% and 74.00%, respectively, on the CPLM 4.0 independent test dataset. In addition, this novel platform uses contextualized embeddings obtained from a pre-trained protein language model, ProtT5-XL-UniRef50 to identify SUMO2/3-specific conjugation sites. The results demonstrate that SumoPred-PLM is a powerful and unique computational tool to predict SUMOylation sites in proteins and accelerate discovery. © 2024 The Author(s). Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]
The PKC, HOG and Ca2+ signalling pathways co-ordinately regulate chitin synthesis in Candida albicans
No full textOpen Access via PMC2649417Peer reviewe
Spatially regulated editing of genetic information within a neuron
No full text© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Vallecillo-Viejo, I. C., Liscovitch-Brauer, N., Diaz Quiroz, J. F., Montiel-Gonzalez, Maria F., Nemes, Sonya E., Rangan, K. J., Levinson, S. R., Eisenberg, E., & Rosenthal, J. J. C. Spatially regulated editing of genetic information within a neuron. Nucleic Acids Research, (2020): gkaa172, doi: 10.1093/nar/gkaa172.In eukaryotic cells, with the exception of the specialized genomes of mitochondria and plastids, all genetic information is sequestered within the nucleus. This arrangement imposes constraints on how the information can be tailored for different cellular regions, particularly in cells with complex morphologies like neurons. Although messenger RNAs (mRNAs), and the proteins that they encode, can be differentially sorted between cellular regions, the information itself does not change. RNA editing by adenosine deamination can alter the genome’s blueprint by recoding mRNAs; however, this process too is thought to be restricted to the nucleus. In this work, we show that ADAR2 (adenosine deaminase that acts on RNA), an RNA editing enzyme, is expressed outside of the nucleus in squid neurons. Furthermore, purified axoplasm exhibits adenosine-to-inosine activity and can specifically edit adenosines in a known substrate. Finally, a transcriptome-wide analysis of RNA editing reveals that tens of thousands of editing sites (>70% of all sites) are edited more extensively in the squid giant axon than in its cell bodies. These results indicate that within a neuron RNA editing can recode genetic information in a region-specific manner.National Science Foundation (NSF) [IOS1557748 to J.R.]; United States–Israel Binational Science Foundation [BSF2013094 to J.R. and E.E.]; The Grass Foundation grant in support of the Doryteuthis pealeii Genome Project, and a gift by Mr. Edward Owens. Funding for open access charge: United States–Israel Binational Science Foundation [BSF2013094]
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